tests/testthat/test_Matched.R
In rformassspectrometry/MetaboAnnotation: Utilities for Annotation of Metabolomics Data
q1 <- data.frame(col1 = 1:5, col2 = 6:10)
t1 <- data.frame(col1 = 11:16, col2 = 17:22)
q2 <- list("A", c(1,2), 1L, list(), data.frame())
t2 <- list("A", c(1,2), 1L, list(), data.frame(), matrix(1:3))
library(SummarizedExperiment)
q3 <- SummarizedExperiment(assays = data.frame(matrix(NA, 5, 2)),
rowData = q1,
colData = data.frame(cD1 = c(NA, NA),
cD2 = c(NA, NA)))
library(QFeatures)
q4 <- QFeatures(list(a1 = q3, a2 = q3[4:5]))
t3 <- t4 <- t1
m <- data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1))
test_that("validator work", {
## .validate_matches_format
res <- .validate_matches_format(4)
expect_match(res, "data.frame")
res <- .validate_matches_format(data.frame())
expect_match(res, "Not all ")
tmp <- data.frame(query_idx = 1:3, target_idx = 1:6, score = 12)
res <- .validate_matches_format(tmp)
expect_equal(res, NULL)
tmp$query_idx <- "a"
res <- .validate_matches_format(tmp)
expect_match(res, "query_idx")
tmp$query_idx <- 1:6
tmp$target_idx <- "a"
res <- .validate_matches_format(tmp)
expect_match(res, "target_idx")
## .validate_matches_content
tmp$target_idx <- c(1:3, 1:3)
res <- .validate_matches_content(tmp, 3, 3)
expect_match(res, "query_idx")
res <- .validate_matches_content(tmp, 9, 2)
expect_match(res, "target_idx")
res <- .validate_matches_content(tmp, 10, 10)
expect_equal(res, NULL)
## .validate_qt
q <- matrix(rep(1,4),2,2)
res <- .validate_qt(q)
expect_match(res, "no column names")
colnames(q) <- c("col1", "col2")
res <- .validate_qt(q)
expect_equal(res, NULL)
q <- array(rep(1,8), dim = c(2,2,2))
res <- .validate_qt(q)
expect_match(res, "unsupported dimensions ")
})
test_that("Matched works", {
mo <- Matched()
expect_true(validObject(mo))
expect_output(show(mo), "Matched")
expect_equal(whichQuery(mo), integer())
expect_equal(whichTarget(mo), integer())
expect_equal(scoreVariables(mo), "score")
expect_equal(queryVariables(mo), "query")
expect_equal(targetVariables(mo), "target")
## With data. query and target of type data.frame
mo <- Matched(query = q1, target = t1,
matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
expect_true(validObject(mo))
expect_true(length(mo) == 5)
expect_output(show(mo), "4 matched")
expect_true(is(query(mo), "data.frame"))
expect_true(is(target(mo), "data.frame"))
expect_equal(whichQuery(mo), c(1L, 2L, 5L))
expect_equal(whichTarget(mo), c(2L, 3L, 4L, 5L))
expect_equal(scoreVariables(mo), c("score"))
expect_equal(queryVariables(mo), colnames(q1))
expect_equal(targetVariables(mo), paste0("target_", colnames(t1)))
## With data. query and target of type list
mo <- Matched(query = q2, target = t2,
matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
expect_true(validObject(mo))
expect_true(length(mo) == 5)
expect_output(show(mo), "4 matched")
expect_true(is(query(mo), "list"))
expect_true(is(target(mo), "list"))
expect_equal(whichQuery(mo), c(1L, 2L, 5L))
expect_equal(whichTarget(mo), c(2L, 3L, 4L, 5L))
expect_equal(scoreVariables(mo), "score")
expect_equal(queryVariables(mo), "query")
expect_equal(targetVariables(mo), "target")
## With data. query SummarizedExperiment and target data.frame
mo <- Matched(query = q3, target = t3,
matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
expect_true(validObject(mo))
expect_true(length(mo) == 5)
expect_output(show(mo), "4 matched")
expect_true(is(query(mo), "SummarizedExperiment"))
expect_true(is(target(mo), "data.frame"))
expect_equal(whichQuery(mo), c(1L, 2L, 5L))
expect_equal(whichTarget(mo), c(2L, 3L, 4L, 5L))
expect_equal(scoreVariables(mo), "score")
expect_equal(queryVariables(mo), colnames(rowData(q3)))
expect_equal(targetVariables(mo), paste0("target_", colnames(t3)))
})
test_that(".subset_matches_nodim and [ works", {
mo <- Matched()
expect_error(.subset_matches_nodim(mo, 1), "out-of-bounds")
#### query and target: data.frames
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
res <- .subset_matches_nodim(mo, 2)
expect_true(length(res) == 1)
expect_equal(res@matches$query_idx, c(1L, 1L, 1L))
expect_equal(res@matches$target_idx, mo@matches$target_idx[c(2, 3, 4)])
expect_equal(res@matches$score, mo@matches$score[c(2, 3, 4)])
expect_equal(res@query, mo@query[2, ])
expect_equal(res@target, mo@target)
## No matching
res <- .subset_matches_nodim(mo, c(3, 4))
expect_true(validObject(res))
expect_true(nrow(res@matches) == 0)
expect_equal(res@query, mo@query[c(3, 4), ])
expect_error(.subset_matches_nodim(mo, 12), "out-of-bounds")
res <- .subset_matches_nodim(mo, c(1, 5))
expect_equal(res@query, mo@query[c(1, 5), ])
expect_true(length(res) == 2)
expect_equal(res@matches$score, mo@matches$score[c(1, 5)])
## arbitrary order
res <- .subset_matches_nodim(mo, c(3, 2, 1, 1, 4))
expect_equal(query(res), query(mo)[c(3, 2, 1, 1, 4), ])
expect_equal(target(res), target(mo))
expect_equal(res@matches$query_idx, c(2L, 2L, 2L, 3L, 4L))
expect_equal(res@matches$score, c(0.6, 0.7, 0.8, 0.5, 0.5))
res <- mo[]
expect_equal(res, mo)
res <- mo[c(TRUE, FALSE)]
expect_equal(res@matches$query_idx, 1L)
expect_equal(res@matches$target_idx, 2L)
expect_equal(res@matches$score, 0.5)
## All works even after subsetting and pruning.
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
res <- mo[whichQuery(mo)]
expect_equal(query(res), q1[whichQuery(mo), ])
res <- pruneTarget(res)
expect_equal(target(res), t1[c(2, 3, 4, 5), ])
expect_equal(res@matches$target_idx, c(1L, 1L, 2L, 3L, 4L))
#### query and target: lists
mo <- Matched(
q2, t2, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
res <- .subset_matches_nodim(mo, 2)
expect_true(length(res) == 1)
expect_equal(res@matches$query_idx, c(1L, 1L, 1L))
expect_equal(res@matches$target_idx, mo@matches$target_idx[c(2, 3, 4)])
expect_equal(res@matches$score, mo@matches$score[c(2, 3, 4)])
expect_equal(res@query, mo@query[2])
expect_equal(res@target, mo@target)
expect_error(.subset_matches_nodim(mo, 12), "out-of-bounds")
res <- .subset_matches_nodim(mo, c(1, 5))
expect_equal(res@query, mo@query[c(1, 5)])
expect_true(length(res) == 2)
expect_equal(res@matches$score, mo@matches$score[c(1, 5)])
## arbitrary order
res <- .subset_matches_nodim(mo, c(3, 2, 1, 1, 4))
expect_equal(query(res), query(mo)[c(3, 2, 1, 1, 4)])
expect_equal(target(res), target(mo))
expect_equal(res@matches$query_idx, c(2L, 2L, 2L, 3L, 4L))
expect_equal(res@matches$score, c(0.6, 0.7, 0.8, 0.5, 0.5))
res <- mo[]
expect_equal(res, mo)
res <- mo[c(TRUE, FALSE)]
expect_equal(res@matches$query_idx, 1L)
expect_equal(res@matches$target_idx, 2L)
expect_equal(res@matches$score, 0.5)
## All works even after subsetting and pruning.
mo <- Matched(
q2, t2, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
res <- mo[whichQuery(mo)]
expect_equal(query(res), q2[whichQuery(mo)])
res <- pruneTarget(res)
expect_equal(target(res), t2[c(2, 3, 4, 5)])
expect_equal(res@matches$target_idx, c(1L, 1L, 2L, 3L, 4L))
#### query SummarizedExperiment and target data.frame
mo <- Matched(
q3, t3, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
res <- .subset_matches_nodim(mo, 2)
expect_true(length(res) == 1)
expect_equal(res@matches$query_idx, c(1L, 1L, 1L))
expect_equal(res@matches$target_idx, mo@matches$target_idx[c(2, 3, 4)])
expect_equal(res@matches$score, mo@matches$score[c(2, 3, 4)])
expect_equal(res@query, mo@query[2, ])
expect_equal(res@target, mo@target)
expect_error(.subset_matches_nodim(mo, 12), "out-of-bounds")
res <- .subset_matches_nodim(mo, c(1, 5))
expect_equal(res@query, mo@query[c(1, 5), ])
expect_true(length(res) == 2)
expect_equal(res@matches$score, mo@matches$score[c(1, 5)])
## arbitrary order
res <- .subset_matches_nodim(mo, c(3, 2, 1, 1, 4))
expect_equal(query(res), query(mo)[c(3, 2, 1, 1, 4), ])
expect_equal(target(res), target(mo))
expect_equal(res@matches$query_idx, c(2L, 2L, 2L, 3L, 4L))
expect_equal(res@matches$score, c(0.6, 0.7, 0.8, 0.5, 0.5))
res <- mo[]
expect_equal(res, mo)
res <- mo[c(TRUE, FALSE)]
expect_equal(res@matches$query_idx, 1L)
expect_equal(res@matches$target_idx, 2L)
expect_equal(res@matches$score, 0.5)
## All works even after subsetting and pruning.
mo <- Matched(
q3, t3, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
res <- mo[whichQuery(mo)]
expect_equal(query(res), q3[whichQuery(mo), ])
res <- pruneTarget(res)
expect_equal(target(res), t3[c(2, 3, 4, 5), ])
expect_equal(res@matches$target_idx, c(1L, 1L, 2L, 3L, 4L))
})
test_that(".fill_index works", {
res <- .fill_index(1:5, integer())
expect_equal(res, 1:5)
res <- .fill_index(1:20, c(2, 4, 4, 4, 6, 9, 10))
expect_equal(res, c(1, 2, 3, 4, 4, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
14, 15, 16, 17, 18, 19, 20))
})
test_that("$,Matched and .dollar works", {
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
expect_equal(mo$score, c(0.5, 0.6, 0.7, 0.8, NA, NA, 0.9))
expect_equal(mo$score, .dollar(mo@query, mo@target, mo@matches, "score"))
expect_equal(mo$col1, q1[c(1, 2, 2, 2, 3, 4, 5), "col1"])
expect_equal(mo$col1, .dollar(mo@query, mo@target, mo@matches, "col1"))
expect_equal(mo$target_col1, t1[c(2,2,3,4, NA, NA, 5), "col1"])
expect_equal(mo$target_col1,
.dollar(mo@query, mo@target, mo@matches, "target_col1"))
mo <- Matched(
q2, t2, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
expect_equal(mo$score, c(0.5, 0.6, 0.7, 0.8, NA, NA, 0.9))
expect_equal(mo$query, q2[c(1, 2, 2, 2, 3, 4, 5)])
tmp <- t2[c(2,2,3,4, NA, NA, 5)]
tmp[5:6] <- NA
expect_equal(mo$target, tmp)
mo <- Matched(
q2, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
expect_equal(mo$score, c(0.5, 0.6, 0.7, 0.8, NA, NA, 0.9))
expect_equal(mo$query, q2[c(1, 2, 2, 2, 3, 4, 5)])
expect_equal(mo$target_col1, t1[c(2,2,3,4, NA, NA, 5), "col1"])
mo <- Matched(
q1, t2, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
expect_equal(mo$score, c(0.5, 0.6, 0.7, 0.8, NA, NA, 0.9))
expect_equal(mo$col1, q1[c(1, 2, 2, 2, 3, 4, 5), "col1"])
tmp <- t2[c(2,2,3,4, NA, NA, 5)]
tmp[5:6] <- NA
expect_equal(mo$target, tmp)
mo <- Matched(
q3, t3, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
expect_equal(mo$score, c(0.5, 0.6, 0.7, 0.8, NA, NA, 0.9))
expect_equal(mo$col1, rowData(q3)[c(1, 2, 2, 2, 3, 4, 5), "col1"])
expect_equal(mo$target_col1, t3[c(2,2,3,4, NA, NA, 5), "col1"])
})
test_that(".dollar works with unordered @matches", {
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
## Both query and target idx are unsorted.
mo2 <- mo
mo2@matches <- mo@matches[c(2, 1, 3, 5, 4), ]
## query
expect_equal(mo$col1, mo2$col1)
expect_equal(mo$col2, mo2$col2)
## matches
expect_equal(mo$score, mo2$score)
## target
expect_equal(mo$target_col1, mo2$target_col1)
expect_equal(mo$target_col2, mo2$target_col2)
## query idx is sorted, target idx not.
mo2 <- mo
mo2@target <- mo@target[c(4, 5, 1, 2, 3, 6), ]
mo2@matches$target_idx <- c(4L, 4L, 5L, 1L, 2L)
## matches
expect_equal(mo$score, mo2$score)
## target
expect_equal(mo$target_col1, mo2$target_col1)
expect_equal(mo$target_col2, mo2$target_col2)
})
test_that("colnames,Matched works", {
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
expect_equal(colnames(mo), c(colnames(q1),
paste0("target_", colnames(t1)), "score"))
mo <- Matched(
q2, t2, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
expect_equal(colnames(mo), c("query", "target", "score"))
mo <- Matched(
q1, t2, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
expect_equal(colnames(mo), c(colnames(q1), "target", "score"))
mo <- Matched(
q2, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
expect_equal(colnames(mo), c("query",
paste0("target_", colnames(t1)), "score"))
mo <- Matched(
q3, t3, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
expect_equal(colnames(mo), c(colnames(rowData(q3)),
paste0("target_", colnames(t3)), "score"))
})
test_that("matchedData,Matched works", {
mo <- Matched()
res <- matchedData(mo)
expect_true(is(res, "DataFrame"))
expect_true(nrow(res) == 0)
expect_equal(colnames(res), colnames(mo))
#### query and target data.frames
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
res <- matchedData(mo)
expect_equal(res$col2, mo$col2)
expect_equal(res$target_col2, mo$target_col2)
expect_equal(res$score, mo$score)
expect_error(matchedData(mo, columns = "other"), "other not available")
## Only query object variables
res <- matchedData(mo, columns = c("col1", "col2"))
expect_equal(colnames(res), c("col1", "col2"))
expect_equal(res$col1, mo$col1)
## Only target object variables
res <- matchedData(mo, columns = c("target_col1", "target_col2"))
expect_equal(colnames(res), c("target_col1", "target_col2"))
expect_equal(res$target_col1, mo$target_col1)
## Only matches
res <- matchedData(mo, columns = c("score"))
expect_equal(colnames(res), c("score"))
expect_equal(res$score, mo$score)
## A Matched with no matching target elements (query and target data.frames)
mo <- Matched(q1, t1, matches = data.frame(query_idx = integer(),
target_idx = integer(),
score = numeric()))
res <- matchedData(mo)
expect_equal(res$col2, mo$col2)
expect_equal(res$target_col2, mo$target_col2)
expect_equal(res$score, mo$score)
## Only query object variables
res <- matchedData(mo, columns = c("col1", "col2"))
expect_equal(colnames(res), c("col1", "col2"))
expect_equal(res$col1, mo$col1)
## Only target object variables
res <- matchedData(mo, columns = c("target_col1", "target_col2"))
expect_equal(colnames(res), c("target_col1", "target_col2"))
expect_equal(res$target_col1, mo$target_col1)
## Only matches
res <- matchedData(mo, columns = c("score"))
expect_equal(colnames(res), c("score"))
expect_equal(res$score, mo$score)
#### query data.frame and target list
mo <- Matched(
q1, t2, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
res <- matchedData(mo)
expect_equal(res$col2, mo$col2)
expect_equal(res$target, I(mo$target))
expect_equal(res$score, mo$score)
## Only query object variables
res <- matchedData(mo, columns = c("col1", "col2"))
expect_equal(colnames(res), c("col1", "col2"))
expect_equal(res$col1, mo$col1)
## Only target object variables
res <- matchedData(mo, columns = c("target"))
expect_equal(colnames(res), c("target"))
expect_equal(res$target, mo$target)
## Only matches
res <- matchedData(mo, columns = c("score"))
expect_equal(colnames(res), c("score"))
expect_equal(res$score, mo$score)
#### A Matched with no matching target elements: query list and target
#### data.frame
mo <- Matched(q2, t1, matches = data.frame(query_idx = integer(),
target_idx = integer(),
score = numeric()))
res <- matchedData(mo)
expect_equal(res$query, I(mo$query))
expect_equal(res$target_col1, mo$target_col1)
expect_equal(res$score, mo$score)
## Only query object variables
res <- matchedData(mo, columns = c("query"))
expect_equal(colnames(res), c("query"))
expect_equal(res$query, mo$query)
expect_equal(res$query, q2)
## Only target object variables
res <- matchedData(mo, columns = c("target_col1", "target_col2"))
expect_equal(colnames(res), c("target_col1", "target_col2"))
expect_equal(res$target_col1, mo$target_col1)
## Only matches
res <- matchedData(mo, columns = c("score"))
expect_equal(colnames(res), c("score"))
expect_equal(res$score, mo$score)
#### query SummarizedExoeriment and target data.frame
mo <- Matched(
q3, t3, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
res <- matchedData(mo)
expect_equal(res$col2, mo$col2)
expect_equal(res$target_col2, mo$target_col2)
expect_equal(res$score, mo$score)
expect_error(matchedData(mo, columns = "other"), "other not available")
## Only query object variables
res <- matchedData(mo, columns = c("col1", "col2"))
expect_equal(colnames(res), c("col1", "col2"))
expect_equal(res$col1, mo$col1)
## Only target object variables
res <- matchedData(mo, columns = c("target_col1", "target_col2"))
expect_equal(colnames(res), c("target_col1", "target_col2"))
expect_equal(res$target_col1, mo$target_col1)
## Only matches
res <- matchedData(mo, columns = c("score"))
expect_equal(colnames(res), c("score"))
expect_equal(res$score, mo$score)
## A MatchedSummarizedExperiment with no matching target elements
mo <- Matched(q3, t3, matches = data.frame(query_idx = integer(),
target_idx = integer(),
score = numeric()))
res <- matchedData(mo)
expect_equal(res$col2, mo$col2)
expect_equal(res$target_col2, mo$target_col2)
expect_equal(res$score, mo$score)
## Only query object variables
res <- matchedData(mo, columns = c("col1", "col2"))
expect_equal(colnames(res), c("col1", "col2"))
expect_equal(res$col1, mo$col1)
## Only target object variables
res <- matchedData(mo, columns = c("target_col1", "target_col2"))
expect_equal(colnames(res), c("target_col1", "target_col2"))
expect_equal(res$target_col1, mo$target_col1)
## Only matches
res <- matchedData(mo, columns = c("score"))
expect_equal(colnames(res), c("score"))
expect_equal(res$score, mo$score)
})
test_that("pruneTarget,Matched works", {
mo <- Matched()
res <- pruneTarget(mo)
expect_true(is(res, "Matched"))
expect_equal(res, mo)
#### query and target data.frames
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
res <- pruneTarget(mo)
expect_equal(matchedData(res), matchedData(mo))
expect_true(nrow(res@target) < nrow(mo@target))
mo <- Matched(q1, t1, matches = data.frame(query_idx = integer(),
target_idx = integer(),
score = numeric()))
res <- pruneTarget(mo)
expect_equal(matchedData(res), matchedData(mo))
expect_true(nrow(res@target) < nrow(mo@target))
#### query data.frame and target list
mo <- Matched(
q1, t2, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
res <- pruneTarget(mo)
expect_equal(matchedData(res), matchedData(mo))
expect_true(length(res@target) < length(mo@target))
mo <- Matched(q1, t2, matches = data.frame(query_idx = integer(),
target_idx = integer(),
score = numeric()))
res <- pruneTarget(mo)
expect_equal(matchedData(res), matchedData(mo))
expect_true(length(res@target) < length(mo@target))
#### query SummarizedExperiment and target data.frame
mo <- Matched(
q3, t3, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
res <- pruneTarget(mo)
expect_equal(matchedData(res), matchedData(mo))
expect_true(nrow(res@target) < nrow(mo@target))
mo <- Matched(q3, t3, matches = data.frame(query_idx = integer(),
target_idx = integer(),
score = numeric()))
res <- pruneTarget(mo)
expect_equal(matchedData(res), matchedData(mo))
expect_true(nrow(res@target) < nrow(mo@target))
})
test_that("filterMatches,Matched works", {
#### query and target data.frames
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
## out of bounds indexes
expect_error(filterMatches(mo, index = c(1, 10)), "out-of-bounds")
## no index : every match is removed
idxs <- integer(0)
mosub <- filterMatches(mo, index = idxs)
expect_equal(mosub@matches, mo@matches[idxs, ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
expect_s4_class(mosub@metadata[[length(mosub@metadata)]],
"SelectMatchesParam")
## in range indexes
idxs <- c(1, 3, 5)
mosub <- filterMatches(mo, index = idxs)
expect_equal(mosub@matches, mo@matches[idxs, ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
mosub <- filterMatches(mo, index = idxs, keep = FALSE)
expect_equal(mosub@matches, mo@matches[-idxs, ])
## keep matches based on query and target input values
queryValue <- c(q1[mo@matches[idxs, "query_idx"], "col1"], -1, - 2)
targetValue <- c(t1[mo@matches[idxs, "target_idx"], "col2"], -2, -1)
mosub <- filterMatches(mo, queryValue = queryValue,
targetValue = targetValue,
queryColname = "col1", targetColname = "col2")
expect_equal(mosub@matches, mo@matches[idxs, ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
mosub <- filterMatches(mo, queryValue = queryValue,
targetValue = targetValue, queryColname = "col1",
targetColname = "col2", keep = FALSE)
expect_equal(mosub@matches, mo@matches[-idxs, ])
## no matches corresponding to the input values
mosub <- filterMatches(mo, queryValue = queryValue + 100,
targetValue = targetValue + 100,
queryColname = "col1", targetColname = "col2")
expect_equal(mosub@matches, data.frame(query_idx = integer(),
target_idx = integer(),
score = numeric()))
#### query and target vectors (multiple matches corresponding to a given
#### couple of query and target input values)
mo <- Matched(
c(1, 1, 2, 3, 4), c("A", "A", "A", "C", "D"),
matches = data.frame(query_idx = c(1L, 2L, 4L, 5L),
target_idx = c(1L, 2L, 4L, 5L),
score = seq(0.5, 0.8, by = 0.1)))
queryValue <- c(1, 3)
targetValue <- c("A", "C")
mosub <- filterMatches(mo, queryValue = queryValue,
targetValue = targetValue)
expect_equal(mosub@matches, mo@matches[c(1, 2, 3), ])
#### query SummarizedExperiment and target data.frame
mo <- Matched(
q3, t3, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
## out of bounds indexes
expect_error(filterMatches(mo, index = c(1, 10)), "out-of-bounds")
## no index : every match is removed
idxs <- integer(0)
mosub <- filterMatches(mo, index = idxs)
expect_equal(mosub@matches, mo@matches[idxs, ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
## in range indexes
idxs <- c(1, 3, 5)
mosub <- filterMatches(mo, index = idxs)
expect_equal(mosub@matches, mo@matches[idxs, ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
## keep matches based on query and target input values
queryValue <- c(rowData(q3)[mo@matches[idxs, "query_idx"], "col1"], -1, - 2)
targetValue <- c(t3[mo@matches[idxs, "target_idx"], "col2"], -2, -1)
mosub <- filterMatches(mo, queryValue = queryValue,
targetValue = targetValue,
queryColname = "col1", targetColname = "col2")
expect_equal(mosub@matches, mo@matches[idxs, ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
## no matches corresponding to the input values
mosub <- filterMatches(mo, queryValue = queryValue + 100,
targetValue = targetValue + 100,
queryColname = "col1", targetColname = "col2")
expect_equal(mosub@matches, data.frame(query_idx = integer(),
target_idx = integer(),
score = numeric()))
})
test_that("filterMatches,Matched,SelectMatchesParam works", {
#### query and target data.frames
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
## out of bounds indexes
expect_error(filterMatches(mo, SelectMatchesParam(index = c(1L, 10L))),
"out-of-bounds")
## no index : every match is removed
idxs <- integer(0)
mosub <- filterMatches(mo, SelectMatchesParam(index = idxs))
expect_equal(mosub@matches, mo@matches[idxs, ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
expect_s4_class(mosub@metadata[[length(mosub@metadata)]],
"SelectMatchesParam")
## in range indexes
idxs <- c(1L, 3L, 5L)
mosub <- filterMatches(mo, SelectMatchesParam(index = idxs))
expect_equal(mosub@matches, mo@matches[idxs, ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
mosub_old <- filterMatches(mo, index = idxs)
expect_equal(mosub@matches, mosub_old@matches)
mosub <- filterMatches(mo, SelectMatchesParam(index = idxs, keep = FALSE))
expect_equal(mosub@matches, mo@matches[-idxs, ])
## keep matches based on query and target input values
queryValue <- c(q1[mo@matches[idxs, "query_idx"], "col1"], -1, - 2)
targetValue <- c(t1[mo@matches[idxs, "target_idx"], "col2"], -2, -1)
mosub <- filterMatches(mo, SelectMatchesParam(queryValue = queryValue,
targetValue = targetValue,
queryColname = "col1",
targetColname = "col2"))
expect_equal(mosub@matches, mo@matches[idxs, ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
mosub <- filterMatches(mo, SelectMatchesParam(queryValue = queryValue,
targetValue = targetValue,
queryColname = "col1",
targetColname = "col2",
keep = FALSE))
expect_equal(mosub@matches, mo@matches[-idxs, ])
## no matches corresponding to the input values
mosub <- filterMatches(mo,
SelectMatchesParam(queryValue = queryValue + 100,
targetValue = targetValue + 100,
queryColname = "col1",
targetColname = "col2"))
expect_equal(mosub@matches, data.frame(query_idx = integer(),
target_idx = integer(),
score = numeric()))
#### query and target vectors (multiple matches corresponding to a given
#### couple of query and target input values)
mo <- Matched(
c(1, 1, 2, 3, 4), c("A", "A", "A", "C", "D"),
matches = data.frame(query_idx = c(1L, 2L, 4L, 5L),
target_idx = c(1L, 2L, 4L, 5L),
score = seq(0.5, 0.8, by = 0.1)))
queryValue <- c(1, 3)
targetValue <- c("A", "C")
mosub <- filterMatches(mo, SelectMatchesParam(queryValue = queryValue,
targetValue = targetValue))
expect_equal(mosub@matches, mo@matches[c(1, 2, 3), ])
#### query SummarizedExperiment and target data.frame
mo <- Matched(
q3, t3, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
## out of bounds indexes
expect_error(filterMatches(mo, SelectMatchesParam(index = c(1L, 10L))),
"out-of-bounds")
## no index : every match is removed
idxs <- integer(0)
mosub <- filterMatches(mo, SelectMatchesParam(index = idxs))
expect_equal(mosub@matches, mo@matches[idxs, ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
## in range indexes
idxs <- c(1L, 3L, 5L)
mosub <- filterMatches(mo, SelectMatchesParam(index = idxs))
expect_equal(mosub@matches, mo@matches[idxs, ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
## keep matches based on query and target input values
queryValue <- c(rowData(q3)[mo@matches[idxs, "query_idx"], "col1"], -1, - 2)
targetValue <- c(t3[mo@matches[idxs, "target_idx"], "col2"], -2, -1)
mosub <- filterMatches(mo, SelectMatchesParam(queryValue = queryValue,
targetValue = targetValue,
queryColname = "col1",
targetColname = "col2"))
expect_equal(mosub@matches, mo@matches[idxs, ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
## no matches corresponding to the input values
mosub <- filterMatches(mo,
SelectMatchesParam(queryValue = queryValue + 100,
targetValue = targetValue + 100,
queryColname = "col1",
targetColname = "col2"))
expect_equal(mosub@matches, data.frame(query_idx = integer(),
target_idx = integer(),
score = numeric()))
})
test_that("filterMatches,Matched,TopRankedMatchesParam works", {
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = c(4, 4, 1, 3, 1)))
mosub <- filterMatches(mo, TopRankedMatchesParam())
expect_equal(mosub@matches, mo@matches[c(1L, 3L, 5L), ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
expect_s4_class(mosub@metadata[[length(mosub@metadata)]],
"TopRankedMatchesParam")
mosub <- filterMatches(mo, TopRankedMatchesParam(n = 2L))
expect_equal(mosub@matches, mo@matches[c(1L, 3L, 4L, 5L), ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
mosub <- filterMatches(mo, TopRankedMatchesParam(n = 10L))
expect_equal(mosub@matches, mo@matches)
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = c(4, 4, 1, 3, 1),
score_rt = c(1, -1, -1, -2, 1)))
mosub <- filterMatches(mo, TopRankedMatchesParam())
expect_equal(mosub@matches, mo@matches[c(1L, 3L, 5L), ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
mosub <- filterMatches(mo, TopRankedMatchesParam(n = 2L))
expect_equal(mosub@matches, mo@matches[c(1L, 2L, 3L, 5L), ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
mosub <- filterMatches(mo, TopRankedMatchesParam(n = 10L))
expect_equal(mosub@matches, mo@matches)
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
q1 <- data.frame(col1 = 1:5, col2 = 6:10)
t2 <- 11:16
mo <- Matched(q1, t2,
matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
res <- filterMatches(mo, TopRankedMatchesParam(n = 1L))
expect_equal(res@matches$query_idx, c(1, 2, 5))
expect_equal(res@matches$target_idx, c(2, 2, 5))
expect_equal(res@matches$score, c(0.5, 0.6, 0.9))
res <- filterMatches(mo, TopRankedMatchesParam(n = 1L, decreasing = TRUE))
expect_equal(res@matches$query_idx, c(1, 2, 5))
expect_equal(res@matches$target_idx, c(2, 4, 5))
expect_equal(res@matches$score, c(0.5, 0.8, 0.9))
})
test_that("filterMatches,Matched,ScoreThresholdParam works", {
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = c(4, 4, 1, 3, 1)))
mosub <- filterMatches(mo, ScoreThresholdParam())
expect_equal(mosub@matches, mo@matches[integer(0), ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
expect_s4_class(mosub@metadata[[length(mosub@metadata)]],
"ScoreThresholdParam")
mosub <- filterMatches(mo, ScoreThresholdParam(threshold = 2.5))
expect_equal(mosub@matches, mo@matches[c(3L, 5L), ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
mosub <- filterMatches(mo, ScoreThresholdParam(threshold = 2.5,
above = TRUE))
expect_equal(mosub@matches, mo@matches[c(1L, 2L, 4L), ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
expect_error(filterMatches(mo, ScoreThresholdParam(threshold = 2.5,
column = "notpresent")),
"variable not present")
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = c(4, 4, 1, 3, 1),
score_rt = c(1, -1, -1, -2, 1)))
mosub <- filterMatches(mo, ScoreThresholdParam(threshold = 0,
column = "score_rt"))
expect_equal(mosub@matches, mo@matches[c(2L, 3L, 4L), ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
})
test_that("addMatches,Matched works", {
#### query and target data.frames
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
moadd <- addMatches(mo, queryValue = q1[c(3, 5), "col1"],
targetValue = t1[c(1, 6), "col2"],
queryColname = "col1", targetColname = "col2",
score = data.frame(score = c(1, 1.1)), isIndex = FALSE)
expect_equal(moadd@matches$query_idx, c(mo@matches$query_idx, 3, 5))
expect_equal(moadd@matches$target_idx, c(mo@matches$target_idx, 1, 6))
expect_equal(moadd@matches$score, c(mo@matches$score, 1, 1.1))
expect_equal(query(moadd), query(mo))
expect_equal(target(moadd), target(mo))
moadd <- addMatches(mo, queryValue = c(3L, 5L),
targetValue = c(1L, 6L),
queryColname = "col1", targetColname = "col2",
score = data.frame(score = c(1, 1.1)), isIndex = TRUE)
expect_equal(moadd@matches$query_idx, c(mo@matches$query_idx, 3, 5))
expect_equal(moadd@matches$target_idx, c(mo@matches$target_idx, 1, 6))
expect_equal(moadd@matches$score, c(mo@matches$score, 1, 1.1))
expect_equal(query(moadd), query(mo))
expect_equal(target(moadd), target(mo))
#### query vector and target data.frame
mo <- Matched(q1[, "col1"], t1,
matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
moadd <- addMatches(mo, queryValue = c(q1[c(3, 5), "col1"], 50),
targetValue = c(t1[c(1, 6), "col2"], 50),
targetColname = "col2",
score = data.frame(score = c(1, 1.1, 2)))
expect_equal(moadd@matches$query_idx, c(mo@matches$query_idx, 3, 5))
expect_equal(moadd@matches$target_idx, c(mo@matches$target_idx, 1, 6))
expect_equal(moadd@matches$score, c(mo@matches$score, 1, 1.1))
expect_equal(query(moadd), query(mo))
expect_equal(target(moadd), target(mo))
moadd <- addMatches(mo, queryValue = c(3L, 5L),
targetValue = c(1L, 6L), targetColname = "col2",
score = data.frame(score = c(1, 1.1)), isIndex = TRUE)
expect_equal(moadd@matches$query_idx, c(mo@matches$query_idx, 3, 5))
expect_equal(moadd@matches$target_idx, c(mo@matches$target_idx, 1, 6))
expect_equal(moadd@matches$score, c(mo@matches$score, 1, 1.1))
expect_equal(query(moadd), query(mo))
expect_equal(target(moadd), target(mo))
#### query SummarizedExperiment and target data.frame
mo <- Matched(
query = q3, target = t3,
matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
moadd <- addMatches(mo, queryValue = 2L, targetValue = 1L, isIndex = TRUE,
score = data.frame(score = 100))
expect_true(matches(moadd)$query_idx[6] == 2)
expect_true(matches(moadd)$target_idx[6] == 1)
expect_true(matches(moadd)$score[6] == 100)
})
test_that(".extract_elements works", {
a <- data.frame(a = 1:5)
expect_equal(.extract_elements(a, 3)[, 1], 3)
expect_equal(.extract_elements(a, c(3, 6))[, 1], c(3, NA))
expect_equal(.extract_elements(a, c(NA, 1))[, 1], c(NA, 1))
a <- 1:5
expect_equal(.extract_elements(a, 3), 3)
expect_equal(.extract_elements(a, c(3, 6)), c(3, NA))
expect_equal(.extract_elements(a, c(NA, 1)), c(NA, 1))
a <- list(1, 2, 3, 4, 5)
expect_equal(.extract_elements(a, 3), list(3))
expect_equal(.extract_elements(a, c(3, 6)), list(3, NULL))
expect_equal(.extract_elements(a, c(NA, 1)), list(NA, 1))
})
test_that(".cnt works", {
t <- data.frame(a = 1:5, b = 2:6)
expect_equal(.cnt(t), c("target_a", "target_b"))
t <- 1:5
expect_equal(.cnt(t), "target")
t <- array(data = 1, dim = c(1, 1, 1))
expect_error(.cnt(t), "unsupported")
})
test_that(".validate_assay works", {
expect_identical(.validate_assay(q4, c("a1", "a2")),
"`queryAssay` must be `character(1)`")
expect_identical(.validate_assay(q4, "a3", "target"),
"No assay in `target` with name \"a3\"")
expect_null(.validate_assay(q4, "a1"))
})
test_that(".objectToMatch works", {
expect_identical(.objectToMatch(q1), q1)
expect_identical(.objectToMatch(q2), q2)
expect_identical(.objectToMatch(q3), rowData(q3))
expect_error(.objectToMatch(q4), "has to be provided")
expect_error(.objectToMatch(q4, c("a1", "a2")), "must be `character")
expect_error(.objectToMatch(q4, c("a3")), "with name")
expect_identical(.objectToMatch(q4, c("a1")), rowData(q4[["a1"]]))
expect_identical(.objectToMatch(q1, "assayname", "col2"), q1[, "col2"])
expect_identical(.objectToMatch(q3, colnames = "col2"),
rowData(q3)[, "col2"])
expect_identical(.objectToMatch(q4, "a1", "col2"),
rowData(q4[["a1"]])[, "col2"])
expect_error(.objectToMatch(q1, "a1", c("col1", "col3")), "Missing column")
expect_error(.objectToMatch(q3, "a1", c("col1", "col3")), "Missing column")
expect_error(.objectToMatch(q4, "a1", c("col1", "col3")), "Missing column")
expect_error(.objectToMatch(pest_ms2, colnames = c("other_col")),
"Missing spectra")
expect_identical(.objectToMatch(pest_ms2), spectraData(pest_ms2))
expect_identical(.objectToMatch(pest_ms2, colnames = c("rtime", "msLevel")),
spectraData(pest_ms2, c("rtime", "msLevel")))
})
test_that(".subset_qt works", {
i <- c(1, 3)
expect_identical(.subset_qt(q1, i = i), q1[i, ])
expect_identical(.subset_qt(q2, i = i), q2[i])
expect_identical(.subset_qt(q3, i = i), (q3)[i, ])
res <- .subset_qt(q4, "a1", i = i)
expect_is(res, "QFeatures")
expect_equal(res[["a1"]], q4[["a1"]][i, ])
})
test_that("SelectMatchesParam works", {
res <- SelectMatchesParam()
expect_true(is(res, "SelectMatchesParam"))
expect_error(SelectMatchesParam(queryValue = "A", targetValue = 1:2),
"must have the same length")
expect_error(SelectMatchesParam(queryColname = c("A", "b")),
"cannot be of length greater than 1")
expect_error(SelectMatchesParam(targetColname = c("A", "b")),
"cannot be of length greater than 1")
expect_error(SelectMatchesParam(index = c(1L, -2L)),
"must contain positive integers")
expect_error(SelectMatchesParam(keep = rep(TRUE, 2)),
"must be a logical of length 1")
})
test_that("TopRankedMatchesParam works", {
res <- TopRankedMatchesParam()
expect_true(is(res, "TopRankedMatchesParam"))
expect_error(TopRankedMatchesParam(n = c(2L, 3L)), "length 1")
expect_error(TopRankedMatchesParam(n = -4L), "positive integer")
})
test_that("endoapply,Matched works", {
mo <- Matched(
query = data.frame(val = 1:5, name = letters[1:5]),
target = data.frame(val = 11:16, name = LETTERS[1:6]),
matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
fun0 <- function(x, threshold) {
x@matches <- x@matches[x@matches$score < threshold, ]
x
}
res <- endoapply(mo, fun0, threshold = 0.75)
expect_true(is(res, "Matched"))
expect_identical(query(res), query(mo))
expect_identical(target(res), target(mo))
expect_true(all(res$score < 0.75, na.rm = TRUE))
fun1 <- function(x, cmpds_subs) {
x@matches <- x@matches[x@target[x@matches$target_idx, "name"]
%in% cmpds_subs, ]
x
}
res <- endoapply(mo, fun1, cmpds_subs = c("A", "B", "D"))
expect_identical(query(res), query(mo))
expect_identical(target(res), target(mo))
expect_true(all(res$target_name %in% c("A", "B", "D", NA)))
fun2 <- function(x) {
x@matches <- x@matches[which.min(x@matches$score), ]
x
}
res <- endoapply(mo, fun2)
expect_identical(query(res), query(mo))
expect_identical(target(res), target(mo))
expect_identical(res@matches$query_idx, mo@matches[c(1, 2, 5), "query_idx"])
expect_identical(res@matches$target_idx,
mo@matches[c(1, 2, 5), "target_idx"])
expect_identical(res@matches$score, mo@matches[c(1, 2, 5), "score"])
})
test_that("lapply,Matched works", {
mo <- Matched(query = q1, target = t1,
matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
fun0 <- function(x, threshold) {
x@matches[x@matches$score < threshold, "score"]
}
res <- lapply(mo, fun0, threshold = 0.75)
expect_true(is(res, "list"))
expect_identical(length(res), length(mo))
expect_true(all(unlist(res) < 0.75))
})
test_that("scoreVariables,Matched works", {
expect_identical(scoreVariables(Matched()), "score")
mo <- Matched(query = 1:5, target = 1:6,
matches = data.frame(query_idx = 1:5,
target_idx = 1:5,
score = 1:5,
Score2 = 1:5,
thirdscore = 1:5,
other = letters[1:5]))
expect_identical(scoreVariables(mo), c("score", "Score2", "thirdscore"))
})
test_that("targetIndex works", {
a <- Matched()
expect_identical(targetIndex(a), integer())
a@matches <- data.frame(query_idx = c(1L, 1L, 2L),
target_idx = c(2L, 3L, 2L),
score = 1:3)
expect_identical(targetIndex(a), c(2L, 3L, 2L))
expect_error(targetIndex("t"), "'Matched'")
})
test_that("queryIndex works", {
a <- Matched()
expect_identical(queryIndex(a), integer())
a@matches <- data.frame(query_idx = c(1L, 1L, 2L),
target_idx = c(2L, 3L, 2L),
score = 1:3)
expect_identical(queryIndex(a), c(1L, 1L, 2L))
expect_error(queryIndex(4), "'Matched'")
})
test_that("SingleMatchParam works", {
res <- SingleMatchParam()
expect_s4_class(res, "SingleMatchParam")
expect_true(validObject(res))
expect_error(SingleMatchParam(duplicates = "other"), "should be")
res <- SingleMatchParam("closest", column = "other", decreasing = FALSE)
expect_equal(res@duplicates, "closest")
expect_equal(res@column, "other")
expect_equal(res@decreasing, FALSE)
})
test_that("filterMatches,Matched,SingleMatchParam works", {
a <- Matched()
p <- SingleMatchParam(column = "ops")
expect_error(filterMatches(a, p), "not found")
## target is data.frame
a <- Matched(
query = q1, target = t1,
matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
p@duplicates <- "sum"
p@column <- "score"
expect_error(filterMatches(a, p), "has to be one")
p <- SingleMatchParam()
## remove
res <- filterMatches(a, p)
expect_equal(anyDuplicated(res@matches$query_idx), 0L)
expect_equal(res@matches$target_idx, c(2L, 5L))
## closest
p <- SingleMatchParam(duplicates = "closest")
res <- filterMatches(a, p)
expect_equal(anyDuplicated(res@matches$query_idx), 0L)
expect_equal(res@matches$target_idx, c(2L, 2L, 5L))
## top_ranked
p <- SingleMatchParam(duplicates = "top_ranked", column = "target_col2",
decreasing = TRUE)
res <- filterMatches(a, p)
expect_equal(anyDuplicated(res@matches$query_idx), 0L)
expect_equal(res@matches$target_idx, c(2L, 4L, 5L))
## target is vector
a <- Matched(
query = q1, target = c(100, 200, 300, 800),
matches = data.frame(query_idx = c(1L, 1L, 1L, 3L, 3L, 3L, 3L),
target_idx = c(3L, 4L, 1L, 2L, 3L, 1L, 4L),
score = c(1, 2, 4, 3, 1, 2, 7))
)
## remove
p <- SingleMatchParam()
res <- filterMatches(a, p)
expect_equal(anyDuplicated(res@matches$query_idx), 0L)
expect_equal(res@matches$target_idx, integer())
## closest
p <- SingleMatchParam(duplicates = "closest")
res <- filterMatches(a, p)
expect_equal(anyDuplicated(res@matches$query_idx), 0L)
expect_equal(res@matches$target_idx, c(3L, 3L))
## top_ranked
p <- SingleMatchParam(duplicates = "top_ranked", column = "target",
decreasing = FALSE)
res <- filterMatches(a, p)
expect_equal(anyDuplicated(res@matches$query_idx), 0L)
expect_equal(res@matches$target_idx, c(1L, 1L))
## target is SummarizedExperiment
rowData(q3)$new_col <- seq_len(nrow(q1))
a <- Matched(query = q1, target = q3,
matches = data.frame(
query_idx = c(1L, 1L, 1L, 2L, 2L, 3L, 3L, 5L),
target_idx = c(2L, 4L, 5L, 1L, 2L, 3L, 4L, 5L),
score = c(4, 1, 2, 3, 4, 3, 1, 9)))
## remove
p <- SingleMatchParam()
res <- filterMatches(a, p)
expect_equal(anyDuplicated(res@matches$query_idx), 0L)
expect_equal(res@matches$query_idx, 5L)
expect_equal(res@matches$target_idx, 5L)
## closest
p <- SingleMatchParam(duplicates = "closest")
res <- filterMatches(a, p)
expect_equal(anyDuplicated(res@matches$query_idx), 0L)
expect_equal(res@matches$query_idx, c(1L, 2L, 3L, 5L))
expect_equal(res@matches$target_idx, c(4L, 1L, 4L, 5L))
## top_ranked
p <- SingleMatchParam(duplicates = "top_ranked", column = "target_new_col",
decreasing = TRUE)
res <- filterMatches(a, p)
expect_equal(anyDuplicated(res@matches$query_idx), 0L)
expect_equal(res@matches$query_idx, c(1L, 2L, 3L, 5L))
expect_equal(res@matches$target_idx, c(5L, 2L, 4L, 5L))
})
rformassspectrometry/MetaboAnnotation documentation built on Oct. 20, 2024, 7:25 p.m.
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q1 <- data.frame(col1 = 1:5, col2 = 6:10)
t1 <- data.frame(col1 = 11:16, col2 = 17:22)
q2 <- list("A", c(1,2), 1L, list(), data.frame())
t2 <- list("A", c(1,2), 1L, list(), data.frame(), matrix(1:3))
library(SummarizedExperiment)
q3 <- SummarizedExperiment(assays = data.frame(matrix(NA, 5, 2)),
rowData = q1,
colData = data.frame(cD1 = c(NA, NA),
cD2 = c(NA, NA)))
library(QFeatures)
q4 <- QFeatures(list(a1 = q3, a2 = q3[4:5]))
t3 <- t4 <- t1
m <- data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1))
test_that("validator work", {
## .validate_matches_format
res <- .validate_matches_format(4)
expect_match(res, "data.frame")
res <- .validate_matches_format(data.frame())
expect_match(res, "Not all ")
tmp <- data.frame(query_idx = 1:3, target_idx = 1:6, score = 12)
res <- .validate_matches_format(tmp)
expect_equal(res, NULL)
tmp$query_idx <- "a"
res <- .validate_matches_format(tmp)
expect_match(res, "query_idx")
tmp$query_idx <- 1:6
tmp$target_idx <- "a"
res <- .validate_matches_format(tmp)
expect_match(res, "target_idx")
## .validate_matches_content
tmp$target_idx <- c(1:3, 1:3)
res <- .validate_matches_content(tmp, 3, 3)
expect_match(res, "query_idx")
res <- .validate_matches_content(tmp, 9, 2)
expect_match(res, "target_idx")
res <- .validate_matches_content(tmp, 10, 10)
expect_equal(res, NULL)
## .validate_qt
q <- matrix(rep(1,4),2,2)
res <- .validate_qt(q)
expect_match(res, "no column names")
colnames(q) <- c("col1", "col2")
res <- .validate_qt(q)
expect_equal(res, NULL)
q <- array(rep(1,8), dim = c(2,2,2))
res <- .validate_qt(q)
expect_match(res, "unsupported dimensions ")
})
test_that("Matched works", {
mo <- Matched()
expect_true(validObject(mo))
expect_output(show(mo), "Matched")
expect_equal(whichQuery(mo), integer())
expect_equal(whichTarget(mo), integer())
expect_equal(scoreVariables(mo), "score")
expect_equal(queryVariables(mo), "query")
expect_equal(targetVariables(mo), "target")
## With data. query and target of type data.frame
mo <- Matched(query = q1, target = t1,
matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
expect_true(validObject(mo))
expect_true(length(mo) == 5)
expect_output(show(mo), "4 matched")
expect_true(is(query(mo), "data.frame"))
expect_true(is(target(mo), "data.frame"))
expect_equal(whichQuery(mo), c(1L, 2L, 5L))
expect_equal(whichTarget(mo), c(2L, 3L, 4L, 5L))
expect_equal(scoreVariables(mo), c("score"))
expect_equal(queryVariables(mo), colnames(q1))
expect_equal(targetVariables(mo), paste0("target_", colnames(t1)))
## With data. query and target of type list
mo <- Matched(query = q2, target = t2,
matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
expect_true(validObject(mo))
expect_true(length(mo) == 5)
expect_output(show(mo), "4 matched")
expect_true(is(query(mo), "list"))
expect_true(is(target(mo), "list"))
expect_equal(whichQuery(mo), c(1L, 2L, 5L))
expect_equal(whichTarget(mo), c(2L, 3L, 4L, 5L))
expect_equal(scoreVariables(mo), "score")
expect_equal(queryVariables(mo), "query")
expect_equal(targetVariables(mo), "target")
## With data. query SummarizedExperiment and target data.frame
mo <- Matched(query = q3, target = t3,
matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
expect_true(validObject(mo))
expect_true(length(mo) == 5)
expect_output(show(mo), "4 matched")
expect_true(is(query(mo), "SummarizedExperiment"))
expect_true(is(target(mo), "data.frame"))
expect_equal(whichQuery(mo), c(1L, 2L, 5L))
expect_equal(whichTarget(mo), c(2L, 3L, 4L, 5L))
expect_equal(scoreVariables(mo), "score")
expect_equal(queryVariables(mo), colnames(rowData(q3)))
expect_equal(targetVariables(mo), paste0("target_", colnames(t3)))
})
test_that(".subset_matches_nodim and [ works", {
mo <- Matched()
expect_error(.subset_matches_nodim(mo, 1), "out-of-bounds")
#### query and target: data.frames
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
res <- .subset_matches_nodim(mo, 2)
expect_true(length(res) == 1)
expect_equal(res@matches$query_idx, c(1L, 1L, 1L))
expect_equal(res@matches$target_idx, mo@matches$target_idx[c(2, 3, 4)])
expect_equal(res@matches$score, mo@matches$score[c(2, 3, 4)])
expect_equal(res@query, mo@query[2, ])
expect_equal(res@target, mo@target)
## No matching
res <- .subset_matches_nodim(mo, c(3, 4))
expect_true(validObject(res))
expect_true(nrow(res@matches) == 0)
expect_equal(res@query, mo@query[c(3, 4), ])
expect_error(.subset_matches_nodim(mo, 12), "out-of-bounds")
res <- .subset_matches_nodim(mo, c(1, 5))
expect_equal(res@query, mo@query[c(1, 5), ])
expect_true(length(res) == 2)
expect_equal(res@matches$score, mo@matches$score[c(1, 5)])
## arbitrary order
res <- .subset_matches_nodim(mo, c(3, 2, 1, 1, 4))
expect_equal(query(res), query(mo)[c(3, 2, 1, 1, 4), ])
expect_equal(target(res), target(mo))
expect_equal(res@matches$query_idx, c(2L, 2L, 2L, 3L, 4L))
expect_equal(res@matches$score, c(0.6, 0.7, 0.8, 0.5, 0.5))
res <- mo[]
expect_equal(res, mo)
res <- mo[c(TRUE, FALSE)]
expect_equal(res@matches$query_idx, 1L)
expect_equal(res@matches$target_idx, 2L)
expect_equal(res@matches$score, 0.5)
## All works even after subsetting and pruning.
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
res <- mo[whichQuery(mo)]
expect_equal(query(res), q1[whichQuery(mo), ])
res <- pruneTarget(res)
expect_equal(target(res), t1[c(2, 3, 4, 5), ])
expect_equal(res@matches$target_idx, c(1L, 1L, 2L, 3L, 4L))
#### query and target: lists
mo <- Matched(
q2, t2, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
res <- .subset_matches_nodim(mo, 2)
expect_true(length(res) == 1)
expect_equal(res@matches$query_idx, c(1L, 1L, 1L))
expect_equal(res@matches$target_idx, mo@matches$target_idx[c(2, 3, 4)])
expect_equal(res@matches$score, mo@matches$score[c(2, 3, 4)])
expect_equal(res@query, mo@query[2])
expect_equal(res@target, mo@target)
expect_error(.subset_matches_nodim(mo, 12), "out-of-bounds")
res <- .subset_matches_nodim(mo, c(1, 5))
expect_equal(res@query, mo@query[c(1, 5)])
expect_true(length(res) == 2)
expect_equal(res@matches$score, mo@matches$score[c(1, 5)])
## arbitrary order
res <- .subset_matches_nodim(mo, c(3, 2, 1, 1, 4))
expect_equal(query(res), query(mo)[c(3, 2, 1, 1, 4)])
expect_equal(target(res), target(mo))
expect_equal(res@matches$query_idx, c(2L, 2L, 2L, 3L, 4L))
expect_equal(res@matches$score, c(0.6, 0.7, 0.8, 0.5, 0.5))
res <- mo[]
expect_equal(res, mo)
res <- mo[c(TRUE, FALSE)]
expect_equal(res@matches$query_idx, 1L)
expect_equal(res@matches$target_idx, 2L)
expect_equal(res@matches$score, 0.5)
## All works even after subsetting and pruning.
mo <- Matched(
q2, t2, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
res <- mo[whichQuery(mo)]
expect_equal(query(res), q2[whichQuery(mo)])
res <- pruneTarget(res)
expect_equal(target(res), t2[c(2, 3, 4, 5)])
expect_equal(res@matches$target_idx, c(1L, 1L, 2L, 3L, 4L))
#### query SummarizedExperiment and target data.frame
mo <- Matched(
q3, t3, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
res <- .subset_matches_nodim(mo, 2)
expect_true(length(res) == 1)
expect_equal(res@matches$query_idx, c(1L, 1L, 1L))
expect_equal(res@matches$target_idx, mo@matches$target_idx[c(2, 3, 4)])
expect_equal(res@matches$score, mo@matches$score[c(2, 3, 4)])
expect_equal(res@query, mo@query[2, ])
expect_equal(res@target, mo@target)
expect_error(.subset_matches_nodim(mo, 12), "out-of-bounds")
res <- .subset_matches_nodim(mo, c(1, 5))
expect_equal(res@query, mo@query[c(1, 5), ])
expect_true(length(res) == 2)
expect_equal(res@matches$score, mo@matches$score[c(1, 5)])
## arbitrary order
res <- .subset_matches_nodim(mo, c(3, 2, 1, 1, 4))
expect_equal(query(res), query(mo)[c(3, 2, 1, 1, 4), ])
expect_equal(target(res), target(mo))
expect_equal(res@matches$query_idx, c(2L, 2L, 2L, 3L, 4L))
expect_equal(res@matches$score, c(0.6, 0.7, 0.8, 0.5, 0.5))
res <- mo[]
expect_equal(res, mo)
res <- mo[c(TRUE, FALSE)]
expect_equal(res@matches$query_idx, 1L)
expect_equal(res@matches$target_idx, 2L)
expect_equal(res@matches$score, 0.5)
## All works even after subsetting and pruning.
mo <- Matched(
q3, t3, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
res <- mo[whichQuery(mo)]
expect_equal(query(res), q3[whichQuery(mo), ])
res <- pruneTarget(res)
expect_equal(target(res), t3[c(2, 3, 4, 5), ])
expect_equal(res@matches$target_idx, c(1L, 1L, 2L, 3L, 4L))
})
test_that(".fill_index works", {
res <- .fill_index(1:5, integer())
expect_equal(res, 1:5)
res <- .fill_index(1:20, c(2, 4, 4, 4, 6, 9, 10))
expect_equal(res, c(1, 2, 3, 4, 4, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
14, 15, 16, 17, 18, 19, 20))
})
test_that("$,Matched and .dollar works", {
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
expect_equal(mo$score, c(0.5, 0.6, 0.7, 0.8, NA, NA, 0.9))
expect_equal(mo$score, .dollar(mo@query, mo@target, mo@matches, "score"))
expect_equal(mo$col1, q1[c(1, 2, 2, 2, 3, 4, 5), "col1"])
expect_equal(mo$col1, .dollar(mo@query, mo@target, mo@matches, "col1"))
expect_equal(mo$target_col1, t1[c(2,2,3,4, NA, NA, 5), "col1"])
expect_equal(mo$target_col1,
.dollar(mo@query, mo@target, mo@matches, "target_col1"))
mo <- Matched(
q2, t2, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
expect_equal(mo$score, c(0.5, 0.6, 0.7, 0.8, NA, NA, 0.9))
expect_equal(mo$query, q2[c(1, 2, 2, 2, 3, 4, 5)])
tmp <- t2[c(2,2,3,4, NA, NA, 5)]
tmp[5:6] <- NA
expect_equal(mo$target, tmp)
mo <- Matched(
q2, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
expect_equal(mo$score, c(0.5, 0.6, 0.7, 0.8, NA, NA, 0.9))
expect_equal(mo$query, q2[c(1, 2, 2, 2, 3, 4, 5)])
expect_equal(mo$target_col1, t1[c(2,2,3,4, NA, NA, 5), "col1"])
mo <- Matched(
q1, t2, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
expect_equal(mo$score, c(0.5, 0.6, 0.7, 0.8, NA, NA, 0.9))
expect_equal(mo$col1, q1[c(1, 2, 2, 2, 3, 4, 5), "col1"])
tmp <- t2[c(2,2,3,4, NA, NA, 5)]
tmp[5:6] <- NA
expect_equal(mo$target, tmp)
mo <- Matched(
q3, t3, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
expect_equal(mo$score, c(0.5, 0.6, 0.7, 0.8, NA, NA, 0.9))
expect_equal(mo$col1, rowData(q3)[c(1, 2, 2, 2, 3, 4, 5), "col1"])
expect_equal(mo$target_col1, t3[c(2,2,3,4, NA, NA, 5), "col1"])
})
test_that(".dollar works with unordered @matches", {
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
## Both query and target idx are unsorted.
mo2 <- mo
mo2@matches <- mo@matches[c(2, 1, 3, 5, 4), ]
## query
expect_equal(mo$col1, mo2$col1)
expect_equal(mo$col2, mo2$col2)
## matches
expect_equal(mo$score, mo2$score)
## target
expect_equal(mo$target_col1, mo2$target_col1)
expect_equal(mo$target_col2, mo2$target_col2)
## query idx is sorted, target idx not.
mo2 <- mo
mo2@target <- mo@target[c(4, 5, 1, 2, 3, 6), ]
mo2@matches$target_idx <- c(4L, 4L, 5L, 1L, 2L)
## matches
expect_equal(mo$score, mo2$score)
## target
expect_equal(mo$target_col1, mo2$target_col1)
expect_equal(mo$target_col2, mo2$target_col2)
})
test_that("colnames,Matched works", {
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
expect_equal(colnames(mo), c(colnames(q1),
paste0("target_", colnames(t1)), "score"))
mo <- Matched(
q2, t2, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
expect_equal(colnames(mo), c("query", "target", "score"))
mo <- Matched(
q1, t2, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
expect_equal(colnames(mo), c(colnames(q1), "target", "score"))
mo <- Matched(
q2, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
expect_equal(colnames(mo), c("query",
paste0("target_", colnames(t1)), "score"))
mo <- Matched(
q3, t3, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
expect_equal(colnames(mo), c(colnames(rowData(q3)),
paste0("target_", colnames(t3)), "score"))
})
test_that("matchedData,Matched works", {
mo <- Matched()
res <- matchedData(mo)
expect_true(is(res, "DataFrame"))
expect_true(nrow(res) == 0)
expect_equal(colnames(res), colnames(mo))
#### query and target data.frames
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
res <- matchedData(mo)
expect_equal(res$col2, mo$col2)
expect_equal(res$target_col2, mo$target_col2)
expect_equal(res$score, mo$score)
expect_error(matchedData(mo, columns = "other"), "other not available")
## Only query object variables
res <- matchedData(mo, columns = c("col1", "col2"))
expect_equal(colnames(res), c("col1", "col2"))
expect_equal(res$col1, mo$col1)
## Only target object variables
res <- matchedData(mo, columns = c("target_col1", "target_col2"))
expect_equal(colnames(res), c("target_col1", "target_col2"))
expect_equal(res$target_col1, mo$target_col1)
## Only matches
res <- matchedData(mo, columns = c("score"))
expect_equal(colnames(res), c("score"))
expect_equal(res$score, mo$score)
## A Matched with no matching target elements (query and target data.frames)
mo <- Matched(q1, t1, matches = data.frame(query_idx = integer(),
target_idx = integer(),
score = numeric()))
res <- matchedData(mo)
expect_equal(res$col2, mo$col2)
expect_equal(res$target_col2, mo$target_col2)
expect_equal(res$score, mo$score)
## Only query object variables
res <- matchedData(mo, columns = c("col1", "col2"))
expect_equal(colnames(res), c("col1", "col2"))
expect_equal(res$col1, mo$col1)
## Only target object variables
res <- matchedData(mo, columns = c("target_col1", "target_col2"))
expect_equal(colnames(res), c("target_col1", "target_col2"))
expect_equal(res$target_col1, mo$target_col1)
## Only matches
res <- matchedData(mo, columns = c("score"))
expect_equal(colnames(res), c("score"))
expect_equal(res$score, mo$score)
#### query data.frame and target list
mo <- Matched(
q1, t2, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
res <- matchedData(mo)
expect_equal(res$col2, mo$col2)
expect_equal(res$target, I(mo$target))
expect_equal(res$score, mo$score)
## Only query object variables
res <- matchedData(mo, columns = c("col1", "col2"))
expect_equal(colnames(res), c("col1", "col2"))
expect_equal(res$col1, mo$col1)
## Only target object variables
res <- matchedData(mo, columns = c("target"))
expect_equal(colnames(res), c("target"))
expect_equal(res$target, mo$target)
## Only matches
res <- matchedData(mo, columns = c("score"))
expect_equal(colnames(res), c("score"))
expect_equal(res$score, mo$score)
#### A Matched with no matching target elements: query list and target
#### data.frame
mo <- Matched(q2, t1, matches = data.frame(query_idx = integer(),
target_idx = integer(),
score = numeric()))
res <- matchedData(mo)
expect_equal(res$query, I(mo$query))
expect_equal(res$target_col1, mo$target_col1)
expect_equal(res$score, mo$score)
## Only query object variables
res <- matchedData(mo, columns = c("query"))
expect_equal(colnames(res), c("query"))
expect_equal(res$query, mo$query)
expect_equal(res$query, q2)
## Only target object variables
res <- matchedData(mo, columns = c("target_col1", "target_col2"))
expect_equal(colnames(res), c("target_col1", "target_col2"))
expect_equal(res$target_col1, mo$target_col1)
## Only matches
res <- matchedData(mo, columns = c("score"))
expect_equal(colnames(res), c("score"))
expect_equal(res$score, mo$score)
#### query SummarizedExoeriment and target data.frame
mo <- Matched(
q3, t3, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
res <- matchedData(mo)
expect_equal(res$col2, mo$col2)
expect_equal(res$target_col2, mo$target_col2)
expect_equal(res$score, mo$score)
expect_error(matchedData(mo, columns = "other"), "other not available")
## Only query object variables
res <- matchedData(mo, columns = c("col1", "col2"))
expect_equal(colnames(res), c("col1", "col2"))
expect_equal(res$col1, mo$col1)
## Only target object variables
res <- matchedData(mo, columns = c("target_col1", "target_col2"))
expect_equal(colnames(res), c("target_col1", "target_col2"))
expect_equal(res$target_col1, mo$target_col1)
## Only matches
res <- matchedData(mo, columns = c("score"))
expect_equal(colnames(res), c("score"))
expect_equal(res$score, mo$score)
## A MatchedSummarizedExperiment with no matching target elements
mo <- Matched(q3, t3, matches = data.frame(query_idx = integer(),
target_idx = integer(),
score = numeric()))
res <- matchedData(mo)
expect_equal(res$col2, mo$col2)
expect_equal(res$target_col2, mo$target_col2)
expect_equal(res$score, mo$score)
## Only query object variables
res <- matchedData(mo, columns = c("col1", "col2"))
expect_equal(colnames(res), c("col1", "col2"))
expect_equal(res$col1, mo$col1)
## Only target object variables
res <- matchedData(mo, columns = c("target_col1", "target_col2"))
expect_equal(colnames(res), c("target_col1", "target_col2"))
expect_equal(res$target_col1, mo$target_col1)
## Only matches
res <- matchedData(mo, columns = c("score"))
expect_equal(colnames(res), c("score"))
expect_equal(res$score, mo$score)
})
test_that("pruneTarget,Matched works", {
mo <- Matched()
res <- pruneTarget(mo)
expect_true(is(res, "Matched"))
expect_equal(res, mo)
#### query and target data.frames
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
res <- pruneTarget(mo)
expect_equal(matchedData(res), matchedData(mo))
expect_true(nrow(res@target) < nrow(mo@target))
mo <- Matched(q1, t1, matches = data.frame(query_idx = integer(),
target_idx = integer(),
score = numeric()))
res <- pruneTarget(mo)
expect_equal(matchedData(res), matchedData(mo))
expect_true(nrow(res@target) < nrow(mo@target))
#### query data.frame and target list
mo <- Matched(
q1, t2, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
res <- pruneTarget(mo)
expect_equal(matchedData(res), matchedData(mo))
expect_true(length(res@target) < length(mo@target))
mo <- Matched(q1, t2, matches = data.frame(query_idx = integer(),
target_idx = integer(),
score = numeric()))
res <- pruneTarget(mo)
expect_equal(matchedData(res), matchedData(mo))
expect_true(length(res@target) < length(mo@target))
#### query SummarizedExperiment and target data.frame
mo <- Matched(
q3, t3, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
res <- pruneTarget(mo)
expect_equal(matchedData(res), matchedData(mo))
expect_true(nrow(res@target) < nrow(mo@target))
mo <- Matched(q3, t3, matches = data.frame(query_idx = integer(),
target_idx = integer(),
score = numeric()))
res <- pruneTarget(mo)
expect_equal(matchedData(res), matchedData(mo))
expect_true(nrow(res@target) < nrow(mo@target))
})
test_that("filterMatches,Matched works", {
#### query and target data.frames
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
## out of bounds indexes
expect_error(filterMatches(mo, index = c(1, 10)), "out-of-bounds")
## no index : every match is removed
idxs <- integer(0)
mosub <- filterMatches(mo, index = idxs)
expect_equal(mosub@matches, mo@matches[idxs, ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
expect_s4_class(mosub@metadata[[length(mosub@metadata)]],
"SelectMatchesParam")
## in range indexes
idxs <- c(1, 3, 5)
mosub <- filterMatches(mo, index = idxs)
expect_equal(mosub@matches, mo@matches[idxs, ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
mosub <- filterMatches(mo, index = idxs, keep = FALSE)
expect_equal(mosub@matches, mo@matches[-idxs, ])
## keep matches based on query and target input values
queryValue <- c(q1[mo@matches[idxs, "query_idx"], "col1"], -1, - 2)
targetValue <- c(t1[mo@matches[idxs, "target_idx"], "col2"], -2, -1)
mosub <- filterMatches(mo, queryValue = queryValue,
targetValue = targetValue,
queryColname = "col1", targetColname = "col2")
expect_equal(mosub@matches, mo@matches[idxs, ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
mosub <- filterMatches(mo, queryValue = queryValue,
targetValue = targetValue, queryColname = "col1",
targetColname = "col2", keep = FALSE)
expect_equal(mosub@matches, mo@matches[-idxs, ])
## no matches corresponding to the input values
mosub <- filterMatches(mo, queryValue = queryValue + 100,
targetValue = targetValue + 100,
queryColname = "col1", targetColname = "col2")
expect_equal(mosub@matches, data.frame(query_idx = integer(),
target_idx = integer(),
score = numeric()))
#### query and target vectors (multiple matches corresponding to a given
#### couple of query and target input values)
mo <- Matched(
c(1, 1, 2, 3, 4), c("A", "A", "A", "C", "D"),
matches = data.frame(query_idx = c(1L, 2L, 4L, 5L),
target_idx = c(1L, 2L, 4L, 5L),
score = seq(0.5, 0.8, by = 0.1)))
queryValue <- c(1, 3)
targetValue <- c("A", "C")
mosub <- filterMatches(mo, queryValue = queryValue,
targetValue = targetValue)
expect_equal(mosub@matches, mo@matches[c(1, 2, 3), ])
#### query SummarizedExperiment and target data.frame
mo <- Matched(
q3, t3, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
## out of bounds indexes
expect_error(filterMatches(mo, index = c(1, 10)), "out-of-bounds")
## no index : every match is removed
idxs <- integer(0)
mosub <- filterMatches(mo, index = idxs)
expect_equal(mosub@matches, mo@matches[idxs, ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
## in range indexes
idxs <- c(1, 3, 5)
mosub <- filterMatches(mo, index = idxs)
expect_equal(mosub@matches, mo@matches[idxs, ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
## keep matches based on query and target input values
queryValue <- c(rowData(q3)[mo@matches[idxs, "query_idx"], "col1"], -1, - 2)
targetValue <- c(t3[mo@matches[idxs, "target_idx"], "col2"], -2, -1)
mosub <- filterMatches(mo, queryValue = queryValue,
targetValue = targetValue,
queryColname = "col1", targetColname = "col2")
expect_equal(mosub@matches, mo@matches[idxs, ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
## no matches corresponding to the input values
mosub <- filterMatches(mo, queryValue = queryValue + 100,
targetValue = targetValue + 100,
queryColname = "col1", targetColname = "col2")
expect_equal(mosub@matches, data.frame(query_idx = integer(),
target_idx = integer(),
score = numeric()))
})
test_that("filterMatches,Matched,SelectMatchesParam works", {
#### query and target data.frames
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
## out of bounds indexes
expect_error(filterMatches(mo, SelectMatchesParam(index = c(1L, 10L))),
"out-of-bounds")
## no index : every match is removed
idxs <- integer(0)
mosub <- filterMatches(mo, SelectMatchesParam(index = idxs))
expect_equal(mosub@matches, mo@matches[idxs, ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
expect_s4_class(mosub@metadata[[length(mosub@metadata)]],
"SelectMatchesParam")
## in range indexes
idxs <- c(1L, 3L, 5L)
mosub <- filterMatches(mo, SelectMatchesParam(index = idxs))
expect_equal(mosub@matches, mo@matches[idxs, ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
mosub_old <- filterMatches(mo, index = idxs)
expect_equal(mosub@matches, mosub_old@matches)
mosub <- filterMatches(mo, SelectMatchesParam(index = idxs, keep = FALSE))
expect_equal(mosub@matches, mo@matches[-idxs, ])
## keep matches based on query and target input values
queryValue <- c(q1[mo@matches[idxs, "query_idx"], "col1"], -1, - 2)
targetValue <- c(t1[mo@matches[idxs, "target_idx"], "col2"], -2, -1)
mosub <- filterMatches(mo, SelectMatchesParam(queryValue = queryValue,
targetValue = targetValue,
queryColname = "col1",
targetColname = "col2"))
expect_equal(mosub@matches, mo@matches[idxs, ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
mosub <- filterMatches(mo, SelectMatchesParam(queryValue = queryValue,
targetValue = targetValue,
queryColname = "col1",
targetColname = "col2",
keep = FALSE))
expect_equal(mosub@matches, mo@matches[-idxs, ])
## no matches corresponding to the input values
mosub <- filterMatches(mo,
SelectMatchesParam(queryValue = queryValue + 100,
targetValue = targetValue + 100,
queryColname = "col1",
targetColname = "col2"))
expect_equal(mosub@matches, data.frame(query_idx = integer(),
target_idx = integer(),
score = numeric()))
#### query and target vectors (multiple matches corresponding to a given
#### couple of query and target input values)
mo <- Matched(
c(1, 1, 2, 3, 4), c("A", "A", "A", "C", "D"),
matches = data.frame(query_idx = c(1L, 2L, 4L, 5L),
target_idx = c(1L, 2L, 4L, 5L),
score = seq(0.5, 0.8, by = 0.1)))
queryValue <- c(1, 3)
targetValue <- c("A", "C")
mosub <- filterMatches(mo, SelectMatchesParam(queryValue = queryValue,
targetValue = targetValue))
expect_equal(mosub@matches, mo@matches[c(1, 2, 3), ])
#### query SummarizedExperiment and target data.frame
mo <- Matched(
q3, t3, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
## out of bounds indexes
expect_error(filterMatches(mo, SelectMatchesParam(index = c(1L, 10L))),
"out-of-bounds")
## no index : every match is removed
idxs <- integer(0)
mosub <- filterMatches(mo, SelectMatchesParam(index = idxs))
expect_equal(mosub@matches, mo@matches[idxs, ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
## in range indexes
idxs <- c(1L, 3L, 5L)
mosub <- filterMatches(mo, SelectMatchesParam(index = idxs))
expect_equal(mosub@matches, mo@matches[idxs, ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
## keep matches based on query and target input values
queryValue <- c(rowData(q3)[mo@matches[idxs, "query_idx"], "col1"], -1, - 2)
targetValue <- c(t3[mo@matches[idxs, "target_idx"], "col2"], -2, -1)
mosub <- filterMatches(mo, SelectMatchesParam(queryValue = queryValue,
targetValue = targetValue,
queryColname = "col1",
targetColname = "col2"))
expect_equal(mosub@matches, mo@matches[idxs, ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
## no matches corresponding to the input values
mosub <- filterMatches(mo,
SelectMatchesParam(queryValue = queryValue + 100,
targetValue = targetValue + 100,
queryColname = "col1",
targetColname = "col2"))
expect_equal(mosub@matches, data.frame(query_idx = integer(),
target_idx = integer(),
score = numeric()))
})
test_that("filterMatches,Matched,TopRankedMatchesParam works", {
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = c(4, 4, 1, 3, 1)))
mosub <- filterMatches(mo, TopRankedMatchesParam())
expect_equal(mosub@matches, mo@matches[c(1L, 3L, 5L), ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
expect_s4_class(mosub@metadata[[length(mosub@metadata)]],
"TopRankedMatchesParam")
mosub <- filterMatches(mo, TopRankedMatchesParam(n = 2L))
expect_equal(mosub@matches, mo@matches[c(1L, 3L, 4L, 5L), ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
mosub <- filterMatches(mo, TopRankedMatchesParam(n = 10L))
expect_equal(mosub@matches, mo@matches)
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = c(4, 4, 1, 3, 1),
score_rt = c(1, -1, -1, -2, 1)))
mosub <- filterMatches(mo, TopRankedMatchesParam())
expect_equal(mosub@matches, mo@matches[c(1L, 3L, 5L), ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
mosub <- filterMatches(mo, TopRankedMatchesParam(n = 2L))
expect_equal(mosub@matches, mo@matches[c(1L, 2L, 3L, 5L), ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
mosub <- filterMatches(mo, TopRankedMatchesParam(n = 10L))
expect_equal(mosub@matches, mo@matches)
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
q1 <- data.frame(col1 = 1:5, col2 = 6:10)
t2 <- 11:16
mo <- Matched(q1, t2,
matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
res <- filterMatches(mo, TopRankedMatchesParam(n = 1L))
expect_equal(res@matches$query_idx, c(1, 2, 5))
expect_equal(res@matches$target_idx, c(2, 2, 5))
expect_equal(res@matches$score, c(0.5, 0.6, 0.9))
res <- filterMatches(mo, TopRankedMatchesParam(n = 1L, decreasing = TRUE))
expect_equal(res@matches$query_idx, c(1, 2, 5))
expect_equal(res@matches$target_idx, c(2, 4, 5))
expect_equal(res@matches$score, c(0.5, 0.8, 0.9))
})
test_that("filterMatches,Matched,ScoreThresholdParam works", {
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = c(4, 4, 1, 3, 1)))
mosub <- filterMatches(mo, ScoreThresholdParam())
expect_equal(mosub@matches, mo@matches[integer(0), ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
expect_s4_class(mosub@metadata[[length(mosub@metadata)]],
"ScoreThresholdParam")
mosub <- filterMatches(mo, ScoreThresholdParam(threshold = 2.5))
expect_equal(mosub@matches, mo@matches[c(3L, 5L), ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
mosub <- filterMatches(mo, ScoreThresholdParam(threshold = 2.5,
above = TRUE))
expect_equal(mosub@matches, mo@matches[c(1L, 2L, 4L), ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
expect_error(filterMatches(mo, ScoreThresholdParam(threshold = 2.5,
column = "notpresent")),
"variable not present")
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = c(4, 4, 1, 3, 1),
score_rt = c(1, -1, -1, -2, 1)))
mosub <- filterMatches(mo, ScoreThresholdParam(threshold = 0,
column = "score_rt"))
expect_equal(mosub@matches, mo@matches[c(2L, 3L, 4L), ])
expect_equal(query(mosub), query(mo))
expect_equal(target(mosub), target(mo))
})
test_that("addMatches,Matched works", {
#### query and target data.frames
mo <- Matched(
q1, t1, matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
moadd <- addMatches(mo, queryValue = q1[c(3, 5), "col1"],
targetValue = t1[c(1, 6), "col2"],
queryColname = "col1", targetColname = "col2",
score = data.frame(score = c(1, 1.1)), isIndex = FALSE)
expect_equal(moadd@matches$query_idx, c(mo@matches$query_idx, 3, 5))
expect_equal(moadd@matches$target_idx, c(mo@matches$target_idx, 1, 6))
expect_equal(moadd@matches$score, c(mo@matches$score, 1, 1.1))
expect_equal(query(moadd), query(mo))
expect_equal(target(moadd), target(mo))
moadd <- addMatches(mo, queryValue = c(3L, 5L),
targetValue = c(1L, 6L),
queryColname = "col1", targetColname = "col2",
score = data.frame(score = c(1, 1.1)), isIndex = TRUE)
expect_equal(moadd@matches$query_idx, c(mo@matches$query_idx, 3, 5))
expect_equal(moadd@matches$target_idx, c(mo@matches$target_idx, 1, 6))
expect_equal(moadd@matches$score, c(mo@matches$score, 1, 1.1))
expect_equal(query(moadd), query(mo))
expect_equal(target(moadd), target(mo))
#### query vector and target data.frame
mo <- Matched(q1[, "col1"], t1,
matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
moadd <- addMatches(mo, queryValue = c(q1[c(3, 5), "col1"], 50),
targetValue = c(t1[c(1, 6), "col2"], 50),
targetColname = "col2",
score = data.frame(score = c(1, 1.1, 2)))
expect_equal(moadd@matches$query_idx, c(mo@matches$query_idx, 3, 5))
expect_equal(moadd@matches$target_idx, c(mo@matches$target_idx, 1, 6))
expect_equal(moadd@matches$score, c(mo@matches$score, 1, 1.1))
expect_equal(query(moadd), query(mo))
expect_equal(target(moadd), target(mo))
moadd <- addMatches(mo, queryValue = c(3L, 5L),
targetValue = c(1L, 6L), targetColname = "col2",
score = data.frame(score = c(1, 1.1)), isIndex = TRUE)
expect_equal(moadd@matches$query_idx, c(mo@matches$query_idx, 3, 5))
expect_equal(moadd@matches$target_idx, c(mo@matches$target_idx, 1, 6))
expect_equal(moadd@matches$score, c(mo@matches$score, 1, 1.1))
expect_equal(query(moadd), query(mo))
expect_equal(target(moadd), target(mo))
#### query SummarizedExperiment and target data.frame
mo <- Matched(
query = q3, target = t3,
matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
moadd <- addMatches(mo, queryValue = 2L, targetValue = 1L, isIndex = TRUE,
score = data.frame(score = 100))
expect_true(matches(moadd)$query_idx[6] == 2)
expect_true(matches(moadd)$target_idx[6] == 1)
expect_true(matches(moadd)$score[6] == 100)
})
test_that(".extract_elements works", {
a <- data.frame(a = 1:5)
expect_equal(.extract_elements(a, 3)[, 1], 3)
expect_equal(.extract_elements(a, c(3, 6))[, 1], c(3, NA))
expect_equal(.extract_elements(a, c(NA, 1))[, 1], c(NA, 1))
a <- 1:5
expect_equal(.extract_elements(a, 3), 3)
expect_equal(.extract_elements(a, c(3, 6)), c(3, NA))
expect_equal(.extract_elements(a, c(NA, 1)), c(NA, 1))
a <- list(1, 2, 3, 4, 5)
expect_equal(.extract_elements(a, 3), list(3))
expect_equal(.extract_elements(a, c(3, 6)), list(3, NULL))
expect_equal(.extract_elements(a, c(NA, 1)), list(NA, 1))
})
test_that(".cnt works", {
t <- data.frame(a = 1:5, b = 2:6)
expect_equal(.cnt(t), c("target_a", "target_b"))
t <- 1:5
expect_equal(.cnt(t), "target")
t <- array(data = 1, dim = c(1, 1, 1))
expect_error(.cnt(t), "unsupported")
})
test_that(".validate_assay works", {
expect_identical(.validate_assay(q4, c("a1", "a2")),
"`queryAssay` must be `character(1)`")
expect_identical(.validate_assay(q4, "a3", "target"),
"No assay in `target` with name \"a3\"")
expect_null(.validate_assay(q4, "a1"))
})
test_that(".objectToMatch works", {
expect_identical(.objectToMatch(q1), q1)
expect_identical(.objectToMatch(q2), q2)
expect_identical(.objectToMatch(q3), rowData(q3))
expect_error(.objectToMatch(q4), "has to be provided")
expect_error(.objectToMatch(q4, c("a1", "a2")), "must be `character")
expect_error(.objectToMatch(q4, c("a3")), "with name")
expect_identical(.objectToMatch(q4, c("a1")), rowData(q4[["a1"]]))
expect_identical(.objectToMatch(q1, "assayname", "col2"), q1[, "col2"])
expect_identical(.objectToMatch(q3, colnames = "col2"),
rowData(q3)[, "col2"])
expect_identical(.objectToMatch(q4, "a1", "col2"),
rowData(q4[["a1"]])[, "col2"])
expect_error(.objectToMatch(q1, "a1", c("col1", "col3")), "Missing column")
expect_error(.objectToMatch(q3, "a1", c("col1", "col3")), "Missing column")
expect_error(.objectToMatch(q4, "a1", c("col1", "col3")), "Missing column")
expect_error(.objectToMatch(pest_ms2, colnames = c("other_col")),
"Missing spectra")
expect_identical(.objectToMatch(pest_ms2), spectraData(pest_ms2))
expect_identical(.objectToMatch(pest_ms2, colnames = c("rtime", "msLevel")),
spectraData(pest_ms2, c("rtime", "msLevel")))
})
test_that(".subset_qt works", {
i <- c(1, 3)
expect_identical(.subset_qt(q1, i = i), q1[i, ])
expect_identical(.subset_qt(q2, i = i), q2[i])
expect_identical(.subset_qt(q3, i = i), (q3)[i, ])
res <- .subset_qt(q4, "a1", i = i)
expect_is(res, "QFeatures")
expect_equal(res[["a1"]], q4[["a1"]][i, ])
})
test_that("SelectMatchesParam works", {
res <- SelectMatchesParam()
expect_true(is(res, "SelectMatchesParam"))
expect_error(SelectMatchesParam(queryValue = "A", targetValue = 1:2),
"must have the same length")
expect_error(SelectMatchesParam(queryColname = c("A", "b")),
"cannot be of length greater than 1")
expect_error(SelectMatchesParam(targetColname = c("A", "b")),
"cannot be of length greater than 1")
expect_error(SelectMatchesParam(index = c(1L, -2L)),
"must contain positive integers")
expect_error(SelectMatchesParam(keep = rep(TRUE, 2)),
"must be a logical of length 1")
})
test_that("TopRankedMatchesParam works", {
res <- TopRankedMatchesParam()
expect_true(is(res, "TopRankedMatchesParam"))
expect_error(TopRankedMatchesParam(n = c(2L, 3L)), "length 1")
expect_error(TopRankedMatchesParam(n = -4L), "positive integer")
})
test_that("endoapply,Matched works", {
mo <- Matched(
query = data.frame(val = 1:5, name = letters[1:5]),
target = data.frame(val = 11:16, name = LETTERS[1:6]),
matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
fun0 <- function(x, threshold) {
x@matches <- x@matches[x@matches$score < threshold, ]
x
}
res <- endoapply(mo, fun0, threshold = 0.75)
expect_true(is(res, "Matched"))
expect_identical(query(res), query(mo))
expect_identical(target(res), target(mo))
expect_true(all(res$score < 0.75, na.rm = TRUE))
fun1 <- function(x, cmpds_subs) {
x@matches <- x@matches[x@target[x@matches$target_idx, "name"]
%in% cmpds_subs, ]
x
}
res <- endoapply(mo, fun1, cmpds_subs = c("A", "B", "D"))
expect_identical(query(res), query(mo))
expect_identical(target(res), target(mo))
expect_true(all(res$target_name %in% c("A", "B", "D", NA)))
fun2 <- function(x) {
x@matches <- x@matches[which.min(x@matches$score), ]
x
}
res <- endoapply(mo, fun2)
expect_identical(query(res), query(mo))
expect_identical(target(res), target(mo))
expect_identical(res@matches$query_idx, mo@matches[c(1, 2, 5), "query_idx"])
expect_identical(res@matches$target_idx,
mo@matches[c(1, 2, 5), "target_idx"])
expect_identical(res@matches$score, mo@matches[c(1, 2, 5), "score"])
})
test_that("lapply,Matched works", {
mo <- Matched(query = q1, target = t1,
matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
fun0 <- function(x, threshold) {
x@matches[x@matches$score < threshold, "score"]
}
res <- lapply(mo, fun0, threshold = 0.75)
expect_true(is(res, "list"))
expect_identical(length(res), length(mo))
expect_true(all(unlist(res) < 0.75))
})
test_that("scoreVariables,Matched works", {
expect_identical(scoreVariables(Matched()), "score")
mo <- Matched(query = 1:5, target = 1:6,
matches = data.frame(query_idx = 1:5,
target_idx = 1:5,
score = 1:5,
Score2 = 1:5,
thirdscore = 1:5,
other = letters[1:5]))
expect_identical(scoreVariables(mo), c("score", "Score2", "thirdscore"))
})
test_that("targetIndex works", {
a <- Matched()
expect_identical(targetIndex(a), integer())
a@matches <- data.frame(query_idx = c(1L, 1L, 2L),
target_idx = c(2L, 3L, 2L),
score = 1:3)
expect_identical(targetIndex(a), c(2L, 3L, 2L))
expect_error(targetIndex("t"), "'Matched'")
})
test_that("queryIndex works", {
a <- Matched()
expect_identical(queryIndex(a), integer())
a@matches <- data.frame(query_idx = c(1L, 1L, 2L),
target_idx = c(2L, 3L, 2L),
score = 1:3)
expect_identical(queryIndex(a), c(1L, 1L, 2L))
expect_error(queryIndex(4), "'Matched'")
})
test_that("SingleMatchParam works", {
res <- SingleMatchParam()
expect_s4_class(res, "SingleMatchParam")
expect_true(validObject(res))
expect_error(SingleMatchParam(duplicates = "other"), "should be")
res <- SingleMatchParam("closest", column = "other", decreasing = FALSE)
expect_equal(res@duplicates, "closest")
expect_equal(res@column, "other")
expect_equal(res@decreasing, FALSE)
})
test_that("filterMatches,Matched,SingleMatchParam works", {
a <- Matched()
p <- SingleMatchParam(column = "ops")
expect_error(filterMatches(a, p), "not found")
## target is data.frame
a <- Matched(
query = q1, target = t1,
matches = data.frame(query_idx = c(1L, 2L, 2L, 2L, 5L),
target_idx = c(2L, 2L, 3L, 4L, 5L),
score = seq(0.5, 0.9, by = 0.1)))
p@duplicates <- "sum"
p@column <- "score"
expect_error(filterMatches(a, p), "has to be one")
p <- SingleMatchParam()
## remove
res <- filterMatches(a, p)
expect_equal(anyDuplicated(res@matches$query_idx), 0L)
expect_equal(res@matches$target_idx, c(2L, 5L))
## closest
p <- SingleMatchParam(duplicates = "closest")
res <- filterMatches(a, p)
expect_equal(anyDuplicated(res@matches$query_idx), 0L)
expect_equal(res@matches$target_idx, c(2L, 2L, 5L))
## top_ranked
p <- SingleMatchParam(duplicates = "top_ranked", column = "target_col2",
decreasing = TRUE)
res <- filterMatches(a, p)
expect_equal(anyDuplicated(res@matches$query_idx), 0L)
expect_equal(res@matches$target_idx, c(2L, 4L, 5L))
## target is vector
a <- Matched(
query = q1, target = c(100, 200, 300, 800),
matches = data.frame(query_idx = c(1L, 1L, 1L, 3L, 3L, 3L, 3L),
target_idx = c(3L, 4L, 1L, 2L, 3L, 1L, 4L),
score = c(1, 2, 4, 3, 1, 2, 7))
)
## remove
p <- SingleMatchParam()
res <- filterMatches(a, p)
expect_equal(anyDuplicated(res@matches$query_idx), 0L)
expect_equal(res@matches$target_idx, integer())
## closest
p <- SingleMatchParam(duplicates = "closest")
res <- filterMatches(a, p)
expect_equal(anyDuplicated(res@matches$query_idx), 0L)
expect_equal(res@matches$target_idx, c(3L, 3L))
## top_ranked
p <- SingleMatchParam(duplicates = "top_ranked", column = "target",
decreasing = FALSE)
res <- filterMatches(a, p)
expect_equal(anyDuplicated(res@matches$query_idx), 0L)
expect_equal(res@matches$target_idx, c(1L, 1L))
## target is SummarizedExperiment
rowData(q3)$new_col <- seq_len(nrow(q1))
a <- Matched(query = q1, target = q3,
matches = data.frame(
query_idx = c(1L, 1L, 1L, 2L, 2L, 3L, 3L, 5L),
target_idx = c(2L, 4L, 5L, 1L, 2L, 3L, 4L, 5L),
score = c(4, 1, 2, 3, 4, 3, 1, 9)))
## remove
p <- SingleMatchParam()
res <- filterMatches(a, p)
expect_equal(anyDuplicated(res@matches$query_idx), 0L)
expect_equal(res@matches$query_idx, 5L)
expect_equal(res@matches$target_idx, 5L)
## closest
p <- SingleMatchParam(duplicates = "closest")
res <- filterMatches(a, p)
expect_equal(anyDuplicated(res@matches$query_idx), 0L)
expect_equal(res@matches$query_idx, c(1L, 2L, 3L, 5L))
expect_equal(res@matches$target_idx, c(4L, 1L, 4L, 5L))
## top_ranked
p <- SingleMatchParam(duplicates = "top_ranked", column = "target_new_col",
decreasing = TRUE)
res <- filterMatches(a, p)
expect_equal(anyDuplicated(res@matches$query_idx), 0L)
expect_equal(res@matches$query_idx, c(1L, 2L, 3L, 5L))
expect_equal(res@matches$target_idx, c(5L, 2L, 4L, 5L))
})
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